Subtract Only Overlapping Portions of Meshes
I'll let DrRiisTab answer the double boolean method, however I will demonstrate how to do this from the Knife Project method, as it will ultimately get you there, and you will be able to fall back to it, if for some reason the boolean operations don't quite work out for you. As time allows, I will circle back and edit this answer to give you the textual step by steps. Until then you should be able to follow the Screencast Keys with success.







Note: right at the transition, you will have a open mesh, that you may want to close up. I would recommend W >> E(Bridge Edge Loops), see related link if you need help with the nature of Bridge Edgeloops